Question: Where can I find the Agilent Target BED files?
Answer: If you are running the longranger targeted pipeline you will need a bed file defining the captured regions. You can find Agilent Target BED files on the Agilent website.
1. Start by creating an account and logging in:
2. Select the "Find designs" tab and click SureSelect DNA from the dropdown:
3. Select the "Agilent Catalog" tab to display a list of SureSelect related BED files:
4. Click on desired product (e.g. SureSelect Human All Exon V6 r2). A box will open describing the product:
5. Click download (on the top right of above box) and select the box for the file thats ends in the Region.bed suffix, then click download again:
6. A zipped file will download to your computer. Move this file to your Linux server and uncompress it. This BED file can now be used in the longranger targeted pipeline.